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作物学报 ›› 2021, Vol. 47 ›› Issue (1): 42-49.doi: 10.3724/SP.J.1006.2021.04067

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析

孙倩1,2(), 邹枚伶2, 张辰笈2,4, 江思容2,5, Eder Jorge de Oliveira6, 张圣奎7, 夏志强2,3,4,*(), 王文泉2,3,4,5,*(), 李有志1,*()   

  1. 1广西大学生命科学与技术学院 / 亚热带农业生物资源保护与利用国家重点实验室, 广西南宁 530004
    2中国热带农业科学院热带生物技术研究所, 海南海口 571101
    3中国热带农业科学院热带生物组学大数据中心, 海南海口 571101
    4海南大学, 海南海口 570203
    5南京农业大学, 江苏南京 210095
    6Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
    7齐鲁工业大学, 山东济南 250306
  • 收稿日期:2020-03-13 接受日期:2020-08-19 出版日期:2021-01-12 网络出版日期:2020-09-15
  • 通讯作者: 夏志强,王文泉,李有志
  • 作者简介:E-mail: sunqian9595@163.com
  • 基金资助:
    国家重点研发计划项目(2019YFD1001100);国家自然科学基金-CG联合基金项目(31861143005);滇桂黔石漠化地区特色作物产业发展关键技术集成示范项目(SMH2019-2021);中国热带农业科学院基本科研业务费专项(1630052019022)

Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil

SUN Qian1,2(), ZOU Mei-Ling2, ZHANG Chen-Ji2,4, JIANG Si-Rong2,5, Eder Jorge de Oliveira6, ZHANG Sheng-Kui7, XIA Zhi-Qiang2,3,4,*(), WANG Wen-Quan2,3,4,5,*(), LI You-Zhi1,*()   

  1. 1College of Life Science and Technology / State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, Guangxi, China
    2Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
    3Tropical Bio-omics and Big-Data Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
    4Hainan University, Haikou 570203, Hainan, China
    5Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
    6Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
    7Qilu University of Technology, Jinan 250306, Shandong, China
  • Received:2020-03-13 Accepted:2020-08-19 Published:2021-01-12 Published online:2020-09-15
  • Contact: XIA Zhi-Qiang,WANG Wen-Quan,LI You-Zhi
  • Supported by:
    National Key Research and Development Project(2019YFD1001100);National Natural Science Foundation of China-CG Joint Fund(31861143005);Key Technology Integration Demonstration Project of Characteristic Crop Industry Development in the Rocky Desertification Area of Yunnan, Guangxi and Guizhou(SMH2019-2021);Special Fund for Basic Scientific Research Operating Expenses of the Chinese Academy of Tropical Agricultural Sciences(1630052019022)

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摘要：

为了对巴西木薯种质资源进行遗传多样性、亲缘关系和群体遗传结构分析, 本研究利用了7946个SNPs和1997个InDels分子标记, 通过ADMIXTURE软件进行群体结构分析、GCTA软件进行主成分分析。结果显示, 巴西木薯被划分为9个亚群。这与利用PHYLIP进行的聚类分析结果大概一致, 其中亚群1、亚群2、亚群4、亚群6和亚群8能较好地分别聚在一起, 而其他亚群中的样品大致能聚在一起, 且样品间有一定的交叉。巴西木薯种质资源遗传多样性指数(0.274)高于中国、尼日利亚等, 其中巴西木薯亚群5具有相对较高的遗传多样性水平(0.29)。巴西木薯各亚群的群体遗传分化程度较低(群体分化指数在0.03~0.15之间), 但高于中国木薯种质资源的群体分化指数。各木薯材料间的遗传距离变幅为0.084~0.297, 平均遗传距离为0.228。本研究结果可为后续关联分析发掘优良等位基因及引种提供依据。

关键词: 木薯, SNP, InDel, 遗传多样性, 群体结构

Abstract:

As a typical tropical crop, cassava (Manihot esculenta Crantz) has the characteristics of drought resistance, barren resistance, high biomass and so on. In addition to being used for food and forage, it can also be used for production, processing and starch extraction. Due to highly heterozygous cassava genome, breeding is more difficult. Enriching the genetic diversity of cassava germplasm, comprehensively evaluating its genetic background and traits, and discovering superior alleles that control excellent traits are of great significance for cassava breeding in the future. In order to analyze the genetic diversity, genetic relationship and population structure of cassava germplasm in Brazil, 7946 SNPs and 1997 InDels molecular markers were used. Population structure analysis was performed by ADMIXTURE software, and principal component analysis was performed by GCTA software. Brazilian cassava was divided into nine subgroups, and was roughly consistent with the results of cluster analysis using PHYLIP. Among them, subgroup 1, subgroup 2, subgroup 4, subgroup 6, and subgroup 8 could be clustered together respectively, while the samples of other subgroups could be roughly clustered, and there was a certain cross between the samples. The genetic diversity of cassava germplasm in Brazil (0.274) was higher than the genetic diversity level of cassava germplasm in China and Nigeria. Subgroup 5 of Brazil cassava had a relatively high genetic diversity (0.29). The genetic differentiation of subgroups was low (the genetic differentiation vary from 0.03 to 0.15), but higher than domestic cassava germplasm. The genetic distance between cassava accessions varied from 0.084 to 0.297, with the average of 0.228. The results of this study can provide a basis for subsequent association analysis to identify great alleles and introduction.

Key words: cassava, SNP, InDel, genetic diversity, population structure

表1

192份木薯栽培种"

编号
No.		 名称
Name		 编号
No.		 名称
Name		 编号
No.		 名称
Name		 编号
No.		 名称
Name		 编号
No.		 名称
Name		 编号
No.		 名称
Name
001 9624-09 033 BGM0400 065 BGM0783 097 BGM1291 129 BGM1608 161 BGM1942
002 98150-06 034 BGM0405 066 BGM0788 098 BGM1313 130 BGM1615 162 BGM1957
003 BGM0020 035 BGM0408 067 BGM0807 099 BGM1324 131 BGM1622 163 BGM2022
004 BGM0042 036 BGM0425 068 BGM0886 100 BGM1327 132 BGM1626 164 BGM2028
005 BGM0045 037 BGM0428 069 BGM0889 101 BGM1328 133 BGM1640 165 BGM2041
006 BGM0073 038 BGM0436 070 BGM0896 102 BGM1364 134 BGM1662 166 BGM2047
007 BGM0087 039 BGM0443 071 BGM0905 103 BGM1370 135 BGM1667 167 BGM2052
008 BGM0103 040 BGM0451 072 BGM0917 104 BGM1376 136 BGM1668 168 BGM2061
009 BGM0135 041 BGM0452 073 BGM0930 105 BGM1387 137 BGM1672 169 BGM2062
010 BGM0145 042 BGM0467 074 BGM0972 106 BGM1396 138 BGM1679 170 BGM2063
011 BGM0152 043 BGM0495 075 BGM0976 107 BGM1409 139 BGM1682 171 BGM2071
012 BGM0163 044 BGM0501 076 BGM0982 108 BGM1412 140 BGM1684 172 BGM2078
013 BGM0179 045 BGM0507 077 BGM0989 109 BGM1429 141 BGM1690 173 BGM2081
014 BGM0188 046 BGM0523 078 BGM0993 110 BGM1437 142 BGM1697 174 BGM2082
015 BGM0206 047 BGM0540 079 BGM1042 111 BGM1440 143 BGM1698 175 BGM2083
016 BGM0209 048 BGM0542 080 BGM1050 112 BGM1458 144 BGM1704 176 BRS Amansa Burro
017 BGM0211 049 BGM0543 081 BGM1081 113 BGM1485 145 BGM1706 177 BRS Caipira
018 BGM0213 050 BGM0544 082 BGM1106 114 BGM1487 146 BGM1715 178 BRS Dourada
019 BGM0226 051 BGM0550 083 BGM1110 115 BGM1490 147 BGM1722 179 BRS Formosa
020 BGM0250 052 BGM0551 084 BGM1127 116 BGM1495 148 BGM1728 180 BRS Gema Ovo
021 BGM0261 053 BGM0562 085 BGM1153 117 BGM1510 149 BGM1732 181 BRS Jari
022 BGM0264 054 BGM0564 086 BGM1164 118 BGM1524 150 BGM1750 182 BRS Kiriris
023 BGM0269 055 BGM0574 087 BGM1165 119 BGM1535 151 BGM1757 183 BRS Mulatinha
024 BGM0283 056 BGM0600 088 BGM1171 120 BGM1537 152 BGM1760 184 BRS Tapioqueira
025 BGM0288 057 BGM0620 089 BGM1174 121 BGM1539 153 BGM1761 185 BRS Verdinha
026 BGM0331 058 BGM0624 090 BGM1178 122 BGM1549 154 BGM1763 186 Cascuda
027 BGM0336 059 BGM0640 091 BGM1180 123 BGM1552 155 BGM1794 187 Corrente
028 BGM0338 060 BGM0654 092 BGM1193 124 BGM1576 156 BGM1814 188 Eucalipto
029 BGM0352 061 BGM0670 093 BGM1202 125 BGM1581 157 BGM1835 189 Fécula Branca
030 BGM0361 062 BGM0678 094 BGM1226 126 BGM1590 158 BGM1850 190 IAC90
031 BGM0390 063 BGM0726 095 BGM1252 127 BGM1593 159 BGM1883 191 Olho Junto
032 BGM0394 064 BGM0752 096 BGM1281 128 BGM1596 160 BGM1884 192 Valencia

表2

SNPs和InDels的统计"

总数
Total		 间隔区
Intergenic region		 基因上游区
Upstream gene region		 基因下游区
Downstream gene region		 5'端UTR
5' prime UTR variant		 错义突变
Missense variant		 同义突变
Synonymous variant		 移码突变
Frame shift variant		 其他类型
Other types
9443 3287 4005 471 2 845 745 417 171

图1

192份木薯品种的群体遗传结构 a: 利用ADMIXTURE软件对192份木薯材料进行群体结构分析, 计算K为1~12时的CV error。b: K = 9时的群体结构, 在该群体结构中, 每个个体用一根带有9种不同颜色的线表示, 根据颜色的占比推断该品种属于哪个亚群, 红、橙、黄、绿、蓝绿、湖蓝、深蓝、紫、紫红色分别代表亚群1~9。c: 利用高质量变异位点对192份巴西木薯进行主成分分析, 每一个点代表一份样品, 橙色、桔色、黄色、草绿、深绿、天蓝、深蓝、紫和紫红色分别代表亚群1~9 (根据ADMIXTURE软件推断的结果)。"

图2

192份巴西栽培种木薯系统进化树图 淡蓝色、深蓝色、草绿色、深绿色、肉色、橙色、紫红色、红色和紫色分别代表亚群1~9。"

表3

遗传多样性指数(π)的统计"

亚群
Subgroup		 π
1 0.192
2 0.281
3 0.261
4 0.221
5 0.289
6 0.264
7 0.284
8 0.209
9 0.234
整体Entirety 0.274
平均Average 0.248

表4

群体分化指数(Fst)的统计"

亚群Subgroup 1 2 3 4 5 6 7 8 9
1
2 0.065
3 0.081 0.061
4 0.152 0.073 0.112
5 0.053 0.032 0.069 0.062
6 0.058 0.045 0.033 0.086 0.041
7 0.059 0.038 0.054 0.078 0.031 0.045
8 0.139 0.085 0.076 0.119 0.084 0.056 0.080
9 0.058 0.043 0.046 0.083 0.048 0.034 0.038 0.061
[1] El-Sharkawy M A. Cassava biology and physiology. Plant Mol Biol, 2004,56:481-501.
doi: 10.1007/s11103-005-2270-7
[2] Zidenga T, Leyva-Guerrero E, Moon H, Siritunga D, Sayre R. Extending cassava root shelf life via reduction of reactive oxygen species production. Plant Physiol, 2012,159:1396-1407.
pmid: 22711743
[3] Uchechukwu-Agua A D, Caleb O J, Opara U L. Postharvest handling and storage of fresh cassava root and products: a review. Food Bioproc Technol, 2015,8:729-748.
[4] 严华兵, 叶建秋, 李开绵. 中国木薯育种研究进展. 中国农学通报, 2015,31(15):63-70.
Yan H B, Ye J Q, Li K M. Progress of cassava breeding in China. Chin Agric Sci Bull, 2015,31(15):63-70 (in Chinese with English abstract).
[5] 李月仙, 刘倩, 严炜, 宋记明, 段春芳, 沈绍斌, 张林辉, 娄予强, 刘光华. 木薯种质资源在云南的形态多样性及其形态标记聚类分析. 华中农业大学学报, 2018,37(3):10-18.
Li Y X, Liu Q, Yan W, Song J M, Duan C F, Shen S B, Zhang L H, Lou Y Q, Liu G H. Morphological diversity and clustering analysis of cassava germplasm resources in Yunnan province. J Huazhong Agric Univ, 2018,37(3):10-18 (in Chinese with English abstract).
[6] Fregene M A, Suarez M, Mkumbira J, Kulembeka H, Ndedya E, Kulaya A, Mitchel S, Gullberg U, Rosling H, Dixon A G O, Dean R, Kresovich S. Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop. Theor Appl Genet, 2003,107:1083-1093.
doi: 10.1007/s00122-003-1348-3 pmid: 12856084
[7] Ortiz A H T, Rocha V P C, Moiana L D, Gonçalves-Vidigal M C, Galván M Z, Filho P S V. Population structure and genetic diversity in sweet cassava cultivars from Paraná, Brazil. Plant Mol Biol Rep, 2016,34:1153-1166.
[8] Carvalho L J C B, Schaal B A. Assessing genetic diversity in the cassava (Manihot esculenta Crantz) germplasm collection in Brazil using PCR-based markers. Euphytica, 2001,120:133-142.
doi: 10.1023/A:1017548930235
[9] Pradhan S K, Barik S R, Sahoo A, Mohapatra S, Nayak D K, Mahender A, Meher J, Anandan A, Pandit E. Population structure, genetic diversity and molecular marker trait association analysis for high temperature stress tolerance in rice. PLoS One, 2016,11:e0160027.
pmid: 27494320
[10] Dhanapala A P, Rayb J D, Singhc S K, Hoyos-Villegasd V, Smithb J R, Purcelle L C, Kinge C A, Fritschi F B. Genome-wide association analysis of diverse soybean genotypes reveals novel markers for nitrogen traits. Plant Genome, 2015,8:1-15.
[11] Murray M G, Thompson W F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res, 1980,8:4321-4326.
doi: 10.1093/nar/8.19.4321 pmid: 7433111
[12] Xia Z Q, Zou M L, Zhang S K, Feng B X, Wang W Q. AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping. Sci Rep, 2014,4:7300.
doi: 10.1038/srep07300 pmid: 25466435
[13] Langmead B, Salzberg S L. Fast gapped-read alignment with Bowtie 2. Nat Methods, 2012,9:357-359.
pmid: 22388286
[14] Ramu P, Esuma W, Kawuki R, Rabbi I Y, Egesi C, Bredeson J V, Bart R S, Verma J, Buckler E S, Lu F. Cassava hapmap: managing genetic load in a clonal crop species. bioRxiv, 2016. doi: https://doi.org/10.1101/077123.
doi: 10.1101/2020.11.24.390039 pmid: 33269350
[15] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics, 2009,25:2078-2079.
doi: 10.1093/bioinformatics/btp352 pmid: 19505943
[16] Cingolani P, Platts A, Wang L L, Coon M, Nguyen T, Wang L, Land S J, Lu X Y, Ruden D M. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 2012,6:80-92.
pmid: 22728672
[17] Yang J, Lee S H, Goddard M E, Visscher P M. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet, 2011,88:76-82.
doi: 10.1016/j.ajhg.2010.11.011 pmid: 21167468
[18] Alexander D H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res, 2009,19:1655-1664.
doi: 10.1101/gr.094052.109 pmid: 19648217
[19] Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A R, Bender D, Maller J, Sklar P, Bakker P I W D, Daly M J, Sham P C. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 2007,81:559-575.
pmid: 17701901
[20] Danecek P, Auton A, Abecasis G, Albers C A, Banks E, DePristo M A, Handsaker R E, Lunter G, Marth G T, Sherry S T, McVean G, Durbin R. The variant call format and VCFtools. Bioinformatics, 2011,27:2156-2158.
pmid: 21653522
[21] Wright S. Evolution and the Genetics of Population 4: Variability Within and Among Natural Populations. Chicago & London: the University of Chicago Press, 1978. p 157.
[22] Flint-Garcia S A, Thornsberry J M, Buckler E S. Structure of linkage disequilibrium in plants. Anuu Rev Plant Biol, 2003,54:357-374.
[23] 张圣奎. 木薯种质资源综合评价及主要农艺性状的全基因组关联分析. 华中农业大学博士学位论文, 湖北武汉, 2018.
Zhang S K. Phenotyping and Genome-wide Association Studies of Important Agronomic Traits in Cassava (Manihot esculenta Cranz). PhD Dissertation of Huazhong Agricultural University, Wuhan, Hubei, China, 2018 (in Chinese with English abstract).
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